Running Comet Search

[Maram El-Azouni]

Hello,

When running Comet, it does not load or search any spectra. I checked my mzML file which looks good. I tried using a different mzML file for which the search was successful on a different computer, but I ran into the same error.

I've attached an image of the error (apologies for the image quality). Any help would be appreciated!

Thanks!

[Eric Deutsch]

Hi Maram, I don’t know what the problem might be exactly. The crucial error message is that Comet did not find any spectra worth searching in your file. There could be a variety of reasons for this. One is that it is DIA data, but I do see “DDA” in the filename, so that seems unlikely. Have you adjusted any parameters?

 

I will note that you are running an ancient version of the TPP. You can see from the screenshot that the version of Comet is from 2018. I do encourage that you use the latest version 7.3 from http://www.tppms.org/

 

Although that may not solve your problem. I suspect that it is more fundamental to the input file or search settings.

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[Jimmy Eng]

Maram,

Can send me the search parameters file that was used?  It is c:\TPP_5.2\data\Maram\200ngHeLaPASEF_2Min_PaSER2023\CometParams_Maram.params.

As Eric mentioned, it's either something with the search settings or the mzML.  If you're able to share both the params file as well as the mzML, through some type of file share if it's too big for an email attachment, that would be ideal.

Jimmy